Starting phenix.real_space_refine on Sun Jun 8 18:32:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bwp_16293/06_2025/8bwp_16293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwp_16293/06_2025/8bwp_16293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bwp_16293/06_2025/8bwp_16293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwp_16293/06_2025/8bwp_16293.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwp_16293/06_2025/8bwp_16293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwp_16293/06_2025/8bwp_16293.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6221 2.51 5 N 1610 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.49, per 1000 atoms: 0.68 Number of scatterers: 9578 At special positions: 0 Unit cell: (77.376, 107.328, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1704 8.00 N 1610 7.00 C 6221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A1401 " Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 73.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.742A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 75 removed outlier: 4.316A pdb=" N GLY A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.769A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 121 removed outlier: 4.157A pdb=" N LEU A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.578A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 Processing helix chain 'A' and resid 150 through 181 removed outlier: 3.956A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.337A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 235 through 246 removed outlier: 3.944A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 282 removed outlier: 3.893A pdb=" N LEU A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 342 removed outlier: 4.369A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.690A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.509A pdb=" N LEU A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.534A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 removed outlier: 4.392A pdb=" N PHE A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.873A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.505A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.647A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 808 removed outlier: 3.708A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.697A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.636A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 4.611A pdb=" N ASP A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'A' and resid 864 through 896 Proline residue: A 870 - end of helix removed outlier: 3.599A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.891A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.724A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.016A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 927 " --> pdb=" O CYS A 923 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 988 through 1007 removed outlier: 3.524A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.772A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1109 through 1116 removed outlier: 3.689A pdb=" N LYS A1115 " --> pdb=" O HIS A1111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1161 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1279 through 1294 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 5.804A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 433 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 413 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 435 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS A 411 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.847A pdb=" N ALA A 476 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 606 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 444 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 4.644A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 5.790A pdb=" N LYS A1059 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A1048 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA A1063 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP A1044 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE A1065 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE A1042 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1046 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A1095 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.451A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3024 1.34 - 1.46: 1607 1.46 - 1.58: 5082 1.58 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 9784 Sorted by residual: bond pdb=" C2 MTX A1401 " pdb=" NA2 MTX A1401 " ideal model delta sigma weight residual 1.341 1.407 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CG LEU A 27 " pdb=" CD1 LEU A 27 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB GLN A 931 " pdb=" CG GLN A 931 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.12e+00 bond pdb=" C8A MTX A1401 " pdb=" N8 MTX A1401 " ideal model delta sigma weight residual 1.348 1.393 -0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" CB ARG A 946 " pdb=" CG ARG A 946 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.09e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12676 1.88 - 3.77: 488 3.77 - 5.65: 75 5.65 - 7.54: 18 7.54 - 9.42: 5 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C THR A 943 " pdb=" N THR A 944 " pdb=" CA THR A 944 " ideal model delta sigma weight residual 120.29 115.76 4.53 1.42e+00 4.96e-01 1.02e+01 angle pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " pdb=" CD ARG A 951 " ideal model delta sigma weight residual 111.30 118.25 -6.95 2.30e+00 1.89e-01 9.12e+00 angle pdb=" CA GLN A 849 " pdb=" CB GLN A 849 " pdb=" CG GLN A 849 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" C HIS A 153 " pdb=" N LEU A 154 " pdb=" CA LEU A 154 " ideal model delta sigma weight residual 120.29 116.07 4.22 1.42e+00 4.96e-01 8.84e+00 angle pdb=" CA ARG A 951 " pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.30e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5411 16.96 - 33.92: 329 33.92 - 50.87: 71 50.87 - 67.83: 17 67.83 - 84.79: 7 Dihedral angle restraints: 5835 sinusoidal: 2341 harmonic: 3494 Sorted by residual: dihedral pdb=" CA LEU A1091 " pdb=" C LEU A1091 " pdb=" N SER A1092 " pdb=" CA SER A1092 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LYS A1021 " pdb=" C LYS A1021 " pdb=" N GLU A1022 " pdb=" CA GLU A1022 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 5832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1187 0.068 - 0.136: 309 0.136 - 0.204: 38 0.204 - 0.272: 3 0.272 - 0.340: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA MTX A1401 " pdb=" N MTX A1401 " pdb=" CB MTX A1401 " pdb=" CT MTX A1401 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA PHE A 258 " pdb=" N PHE A 258 " pdb=" C PHE A 258 " pdb=" CB PHE A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PHE A 24 " pdb=" N PHE A 24 " pdb=" C PHE A 24 " pdb=" CB PHE A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1535 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 26 " -0.020 2.00e-02 2.50e+03 1.55e-02 5.98e+00 pdb=" CG TRP A 26 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 26 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 26 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 26 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 26 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 26 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 26 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 939 " -0.024 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE A 939 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 939 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 939 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 939 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1292 " 0.009 2.00e-02 2.50e+03 1.64e-02 5.40e+00 pdb=" CG TYR A1292 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A1292 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A1292 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A1292 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A1292 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1292 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1292 " 0.027 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1421 2.75 - 3.29: 10324 3.29 - 3.83: 15536 3.83 - 4.36: 18837 4.36 - 4.90: 31944 Nonbonded interactions: 78062 Sorted by model distance: nonbonded pdb=" NH1 ARG A 303 " pdb=" OE1 GLU A 306 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.214 3.040 nonbonded pdb=" O SER A1241 " pdb=" OH TYR A1292 " model vdw 2.219 3.040 nonbonded pdb=" O GLU A 521 " pdb=" OG1 THR A 526 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.247 3.040 ... (remaining 78057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.081 9784 Z= 0.457 Angle : 0.899 9.422 13262 Z= 0.492 Chirality : 0.060 0.340 1538 Planarity : 0.008 0.078 1646 Dihedral : 12.537 84.791 3569 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.48 % Allowed : 1.82 % Favored : 97.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1187 helix: -1.44 (0.15), residues: 769 sheet: 0.56 (0.78), residues: 50 loop : 0.32 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 26 HIS 0.014 0.002 HIS A 172 PHE 0.042 0.004 PHE A 939 TYR 0.028 0.005 TYR A 881 ARG 0.023 0.003 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.22442 ( 609) hydrogen bonds : angle 8.61477 ( 1761) covalent geometry : bond 0.01091 ( 9784) covalent geometry : angle 0.89889 (13262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8467 (t0) cc_final: 0.8211 (t0) REVERT: A 67 GLU cc_start: 0.8510 (tp30) cc_final: 0.8278 (tp30) REVERT: A 200 ASN cc_start: 0.8411 (t0) cc_final: 0.7787 (t0) REVERT: A 206 ASP cc_start: 0.7918 (t70) cc_final: 0.7708 (t70) REVERT: A 276 MET cc_start: 0.8329 (tpp) cc_final: 0.8109 (tpp) REVERT: A 316 LEU cc_start: 0.8398 (tp) cc_final: 0.7992 (tt) REVERT: A 728 TYR cc_start: 0.8546 (t80) cc_final: 0.8310 (t80) REVERT: A 953 ASP cc_start: 0.8492 (m-30) cc_final: 0.7945 (m-30) REVERT: A 985 TYR cc_start: 0.8166 (m-80) cc_final: 0.7717 (m-80) REVERT: A 998 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7020 (mmt-90) REVERT: A 1045 ASN cc_start: 0.9065 (t0) cc_final: 0.8806 (t0) REVERT: A 1104 LEU cc_start: 0.9073 (tp) cc_final: 0.8539 (tp) REVERT: A 1122 GLN cc_start: 0.7517 (tt0) cc_final: 0.6847 (tm-30) REVERT: A 1136 ASP cc_start: 0.7587 (t0) cc_final: 0.6875 (t0) REVERT: A 1196 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7621 (mp10) REVERT: A 1212 ASP cc_start: 0.8769 (t0) cc_final: 0.8278 (m-30) REVERT: A 1253 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8766 (mmtm) outliers start: 5 outliers final: 3 residues processed: 211 average time/residue: 0.2746 time to fit residues: 76.9209 Evaluate side-chains 140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.200255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158859 restraints weight = 11458.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156852 restraints weight = 13259.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158291 restraints weight = 13443.841| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9784 Z= 0.172 Angle : 0.612 7.921 13262 Z= 0.331 Chirality : 0.043 0.182 1538 Planarity : 0.004 0.044 1646 Dihedral : 6.771 82.789 1304 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.92 % Allowed : 7.97 % Favored : 90.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1187 helix: 0.26 (0.18), residues: 788 sheet: 0.55 (0.76), residues: 52 loop : 0.60 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 711 HIS 0.006 0.001 HIS A1225 PHE 0.034 0.002 PHE A 258 TYR 0.023 0.002 TYR A1292 ARG 0.009 0.001 ARG A1220 Details of bonding type rmsd hydrogen bonds : bond 0.05333 ( 609) hydrogen bonds : angle 5.01428 ( 1761) covalent geometry : bond 0.00394 ( 9784) covalent geometry : angle 0.61201 (13262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 706 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7565 (mmt180) REVERT: A 744 MET cc_start: 0.7265 (mmm) cc_final: 0.6839 (mtt) REVERT: A 792 ASN cc_start: 0.8389 (t0) cc_final: 0.8119 (t0) REVERT: A 1016 TYR cc_start: 0.7784 (m-10) cc_final: 0.6674 (m-10) REVERT: A 1136 ASP cc_start: 0.7754 (t0) cc_final: 0.7145 (t70) outliers start: 20 outliers final: 15 residues processed: 193 average time/residue: 0.2174 time to fit residues: 59.1369 Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN A1206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.199309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157781 restraints weight = 11576.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156544 restraints weight = 15356.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158271 restraints weight = 13621.294| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9784 Z= 0.179 Angle : 0.595 7.500 13262 Z= 0.316 Chirality : 0.043 0.181 1538 Planarity : 0.004 0.034 1646 Dihedral : 6.513 86.503 1303 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.26 % Allowed : 11.04 % Favored : 85.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1187 helix: 0.55 (0.18), residues: 785 sheet: 1.18 (0.82), residues: 47 loop : 0.60 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.004 0.001 HIS A 172 PHE 0.033 0.002 PHE A 258 TYR 0.021 0.002 TYR A 289 ARG 0.005 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 609) hydrogen bonds : angle 4.73469 ( 1761) covalent geometry : bond 0.00416 ( 9784) covalent geometry : angle 0.59517 (13262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8659 (tp40) cc_final: 0.8356 (tp40) REVERT: A 67 GLU cc_start: 0.8701 (tp30) cc_final: 0.8388 (tp30) REVERT: A 706 ARG cc_start: 0.7946 (tpp-160) cc_final: 0.7555 (mmt180) REVERT: A 744 MET cc_start: 0.7368 (mmm) cc_final: 0.7026 (mtt) REVERT: A 904 LEU cc_start: 0.8461 (tp) cc_final: 0.8248 (tp) REVERT: A 1016 TYR cc_start: 0.7660 (m-10) cc_final: 0.6679 (m-10) REVERT: A 1122 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7736 (tp40) REVERT: A 1136 ASP cc_start: 0.7928 (t0) cc_final: 0.7363 (t0) outliers start: 34 outliers final: 26 residues processed: 179 average time/residue: 0.2172 time to fit residues: 55.4675 Evaluate side-chains 160 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 115 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1068 GLN A1134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.196204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154952 restraints weight = 11555.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152622 restraints weight = 17065.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154606 restraints weight = 15069.581| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9784 Z= 0.247 Angle : 0.658 8.209 13262 Z= 0.345 Chirality : 0.045 0.259 1538 Planarity : 0.004 0.037 1646 Dihedral : 6.476 88.374 1302 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.84 % Allowed : 12.00 % Favored : 84.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1187 helix: 0.44 (0.18), residues: 788 sheet: 1.07 (0.81), residues: 47 loop : 0.57 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 26 HIS 0.005 0.001 HIS A 831 PHE 0.034 0.002 PHE A 258 TYR 0.026 0.002 TYR A 289 ARG 0.005 0.001 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 609) hydrogen bonds : angle 4.78145 ( 1761) covalent geometry : bond 0.00589 ( 9784) covalent geometry : angle 0.65800 (13262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8680 (tp40) cc_final: 0.8210 (tp-100) REVERT: A 289 TYR cc_start: 0.8172 (m-80) cc_final: 0.7900 (m-80) REVERT: A 706 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.7502 (mmt180) REVERT: A 744 MET cc_start: 0.7215 (mmm) cc_final: 0.6981 (mtt) REVERT: A 904 LEU cc_start: 0.8482 (tp) cc_final: 0.8242 (tp) REVERT: A 1016 TYR cc_start: 0.7716 (m-10) cc_final: 0.6729 (m-10) REVERT: A 1122 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7835 (tp40) REVERT: A 1136 ASP cc_start: 0.7815 (t0) cc_final: 0.7335 (t0) outliers start: 40 outliers final: 33 residues processed: 174 average time/residue: 0.2161 time to fit residues: 53.3534 Evaluate side-chains 167 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.201764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161223 restraints weight = 11352.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157279 restraints weight = 14764.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159609 restraints weight = 12990.204| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9784 Z= 0.131 Angle : 0.559 9.404 13262 Z= 0.293 Chirality : 0.041 0.214 1538 Planarity : 0.004 0.035 1646 Dihedral : 6.275 89.089 1302 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.88 % Allowed : 13.92 % Favored : 83.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1187 helix: 0.81 (0.19), residues: 787 sheet: 1.27 (0.83), residues: 47 loop : 0.56 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1099 HIS 0.004 0.001 HIS A 934 PHE 0.033 0.002 PHE A 258 TYR 0.023 0.001 TYR A 289 ARG 0.006 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 609) hydrogen bonds : angle 4.46186 ( 1761) covalent geometry : bond 0.00287 ( 9784) covalent geometry : angle 0.55860 (13262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8604 (tp40) cc_final: 0.8125 (tp-100) REVERT: A 276 MET cc_start: 0.7905 (mmm) cc_final: 0.7469 (mmm) REVERT: A 289 TYR cc_start: 0.8010 (m-80) cc_final: 0.7764 (m-80) REVERT: A 706 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7420 (mmt180) REVERT: A 744 MET cc_start: 0.7172 (mmm) cc_final: 0.6857 (mtt) REVERT: A 904 LEU cc_start: 0.8390 (tp) cc_final: 0.8187 (tp) REVERT: A 1016 TYR cc_start: 0.7632 (m-10) cc_final: 0.6744 (m-10) REVERT: A 1122 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7457 (tp40) REVERT: A 1136 ASP cc_start: 0.8009 (t0) cc_final: 0.7571 (t0) outliers start: 30 outliers final: 21 residues processed: 165 average time/residue: 0.2255 time to fit residues: 53.2268 Evaluate side-chains 155 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.200790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159914 restraints weight = 11457.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160054 restraints weight = 13839.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161243 restraints weight = 11107.460| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.153 Angle : 0.561 8.516 13262 Z= 0.294 Chirality : 0.041 0.178 1538 Planarity : 0.004 0.042 1646 Dihedral : 6.070 84.435 1302 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.78 % Allowed : 15.07 % Favored : 82.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1187 helix: 0.89 (0.19), residues: 790 sheet: 1.37 (0.84), residues: 47 loop : 0.66 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1099 HIS 0.004 0.001 HIS A 934 PHE 0.034 0.002 PHE A 258 TYR 0.028 0.001 TYR A 289 ARG 0.006 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 609) hydrogen bonds : angle 4.40724 ( 1761) covalent geometry : bond 0.00359 ( 9784) covalent geometry : angle 0.56058 (13262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8596 (tp40) cc_final: 0.8075 (tp-100) REVERT: A 276 MET cc_start: 0.7752 (mmm) cc_final: 0.7444 (mmm) REVERT: A 706 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7411 (mmt180) REVERT: A 744 MET cc_start: 0.7064 (mmm) cc_final: 0.6838 (mtt) REVERT: A 1016 TYR cc_start: 0.7666 (m-10) cc_final: 0.6830 (m-10) REVERT: A 1120 ILE cc_start: 0.8926 (mp) cc_final: 0.8648 (pt) REVERT: A 1122 GLN cc_start: 0.8251 (tm-30) cc_final: 0.8006 (tp40) REVERT: A 1136 ASP cc_start: 0.8054 (t0) cc_final: 0.7687 (t0) outliers start: 29 outliers final: 26 residues processed: 162 average time/residue: 0.2363 time to fit residues: 54.6670 Evaluate side-chains 160 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.200816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159668 restraints weight = 11399.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159971 restraints weight = 13253.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160652 restraints weight = 12377.626| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9784 Z= 0.153 Angle : 0.564 8.388 13262 Z= 0.292 Chirality : 0.041 0.185 1538 Planarity : 0.004 0.037 1646 Dihedral : 5.884 80.067 1302 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 15.83 % Favored : 81.57 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1187 helix: 0.92 (0.19), residues: 791 sheet: 1.31 (0.72), residues: 58 loop : 0.70 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1099 HIS 0.004 0.001 HIS A 934 PHE 0.034 0.002 PHE A 258 TYR 0.034 0.002 TYR A 289 ARG 0.006 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 609) hydrogen bonds : angle 4.35794 ( 1761) covalent geometry : bond 0.00357 ( 9784) covalent geometry : angle 0.56449 (13262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8633 (tp40) cc_final: 0.8153 (tp-100) REVERT: A 241 MET cc_start: 0.7718 (mmm) cc_final: 0.7497 (mmm) REVERT: A 276 MET cc_start: 0.7691 (mmm) cc_final: 0.7455 (mmm) REVERT: A 289 TYR cc_start: 0.8068 (m-80) cc_final: 0.7802 (m-80) REVERT: A 367 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7758 (mt) REVERT: A 706 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7422 (mmt180) REVERT: A 744 MET cc_start: 0.7275 (mmm) cc_final: 0.6979 (mtt) REVERT: A 1016 TYR cc_start: 0.7610 (m-10) cc_final: 0.6815 (m-10) REVERT: A 1136 ASP cc_start: 0.8127 (t0) cc_final: 0.7741 (t0) outliers start: 27 outliers final: 22 residues processed: 154 average time/residue: 0.2362 time to fit residues: 52.1367 Evaluate side-chains 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.203365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163113 restraints weight = 11500.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159653 restraints weight = 11947.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.162043 restraints weight = 12001.789| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.135 Angle : 0.543 7.817 13262 Z= 0.284 Chirality : 0.040 0.176 1538 Planarity : 0.003 0.039 1646 Dihedral : 5.660 72.665 1302 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.78 % Allowed : 16.41 % Favored : 80.81 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1187 helix: 1.05 (0.19), residues: 792 sheet: 1.36 (0.71), residues: 58 loop : 0.73 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1099 HIS 0.003 0.001 HIS A 934 PHE 0.033 0.001 PHE A 258 TYR 0.030 0.001 TYR A 289 ARG 0.006 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 609) hydrogen bonds : angle 4.28146 ( 1761) covalent geometry : bond 0.00310 ( 9784) covalent geometry : angle 0.54285 (13262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8631 (tp40) cc_final: 0.8156 (tp-100) REVERT: A 289 TYR cc_start: 0.8021 (m-80) cc_final: 0.7725 (m-80) REVERT: A 706 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7451 (mmt180) REVERT: A 744 MET cc_start: 0.7551 (mmm) cc_final: 0.7136 (mtt) REVERT: A 1016 TYR cc_start: 0.7513 (m-10) cc_final: 0.6777 (m-10) REVERT: A 1120 ILE cc_start: 0.8819 (mp) cc_final: 0.8471 (pt) REVERT: A 1136 ASP cc_start: 0.8301 (t0) cc_final: 0.7887 (t0) outliers start: 29 outliers final: 26 residues processed: 158 average time/residue: 0.2309 time to fit residues: 51.9652 Evaluate side-chains 157 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.221508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178223 restraints weight = 11917.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173917 restraints weight = 9762.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176262 restraints weight = 9020.667| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9784 Z= 0.164 Angle : 0.585 8.262 13262 Z= 0.302 Chirality : 0.042 0.229 1538 Planarity : 0.004 0.040 1646 Dihedral : 5.598 68.803 1302 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.98 % Allowed : 16.99 % Favored : 80.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1187 helix: 1.02 (0.19), residues: 788 sheet: 1.44 (0.72), residues: 58 loop : 0.72 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1147 HIS 0.003 0.001 HIS A 798 PHE 0.033 0.002 PHE A 258 TYR 0.031 0.002 TYR A1259 ARG 0.008 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 609) hydrogen bonds : angle 4.32609 ( 1761) covalent geometry : bond 0.00386 ( 9784) covalent geometry : angle 0.58498 (13262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8608 (tp40) cc_final: 0.8107 (tp-100) REVERT: A 289 TYR cc_start: 0.8125 (m-80) cc_final: 0.7838 (m-80) REVERT: A 706 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7434 (mmt180) REVERT: A 744 MET cc_start: 0.7238 (mmm) cc_final: 0.6960 (mtt) REVERT: A 1016 TYR cc_start: 0.7598 (m-10) cc_final: 0.6828 (m-10) REVERT: A 1136 ASP cc_start: 0.8269 (t0) cc_final: 0.7901 (t0) outliers start: 31 outliers final: 28 residues processed: 160 average time/residue: 0.2399 time to fit residues: 54.9153 Evaluate side-chains 164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1216 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 69 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 903 HIS ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.224129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.180552 restraints weight = 12064.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.180067 restraints weight = 8949.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.180697 restraints weight = 8389.666| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.127 Angle : 0.561 8.561 13262 Z= 0.290 Chirality : 0.041 0.190 1538 Planarity : 0.004 0.043 1646 Dihedral : 5.377 60.893 1302 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.59 % Allowed : 17.66 % Favored : 79.75 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1187 helix: 1.16 (0.19), residues: 790 sheet: 1.04 (0.61), residues: 75 loop : 0.86 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1147 HIS 0.003 0.001 HIS A 934 PHE 0.032 0.001 PHE A 258 TYR 0.030 0.001 TYR A 289 ARG 0.008 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 609) hydrogen bonds : angle 4.21870 ( 1761) covalent geometry : bond 0.00286 ( 9784) covalent geometry : angle 0.56125 (13262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8557 (tp40) cc_final: 0.8078 (tp-100) REVERT: A 706 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.7463 (mmt180) REVERT: A 744 MET cc_start: 0.7233 (mmm) cc_final: 0.6944 (mtt) REVERT: A 1016 TYR cc_start: 0.7542 (m-10) cc_final: 0.6773 (m-80) REVERT: A 1120 ILE cc_start: 0.8693 (mp) cc_final: 0.8454 (pt) REVERT: A 1136 ASP cc_start: 0.8270 (t0) cc_final: 0.7910 (t0) REVERT: A 1166 MET cc_start: 0.7259 (mmp) cc_final: 0.6784 (mpp) outliers start: 27 outliers final: 24 residues processed: 157 average time/residue: 0.2059 time to fit residues: 46.1583 Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1216 GLN Chi-restraints excluded: chain A residue 1272 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 0.0000 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.0050 chunk 22 optimal weight: 0.0030 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.226314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.185069 restraints weight = 11993.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.182721 restraints weight = 12388.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.184412 restraints weight = 9936.936| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9784 Z= 0.111 Angle : 0.565 9.740 13262 Z= 0.288 Chirality : 0.040 0.205 1538 Planarity : 0.004 0.042 1646 Dihedral : 5.188 53.175 1302 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.82 % Allowed : 18.81 % Favored : 79.37 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1187 helix: 1.28 (0.19), residues: 793 sheet: 1.17 (0.62), residues: 75 loop : 0.87 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1147 HIS 0.004 0.001 HIS A1111 PHE 0.033 0.001 PHE A 258 TYR 0.036 0.001 TYR A 289 ARG 0.008 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 609) hydrogen bonds : angle 4.12524 ( 1761) covalent geometry : bond 0.00237 ( 9784) covalent geometry : angle 0.56540 (13262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.81 seconds wall clock time: 58 minutes 47.57 seconds (3527.57 seconds total)